--- /dev/null
+# Name of your program
+package "RNA2Dfold" # don't use package if you're using automake
+purpose "Compute MFE structure, partition function and representative sample structures of k,l neighborhoods"
+
+# Version of your program
+#version "0.9" # don't use version if you're using automake
+
+
+# command line options passed to gengetopt
+args "--file-name=RNA2Dfold_cmdl --include-getopt --default-optional --func-name=RNA2Dfold_cmdline_parser --arg-struct-name=RNA2Dfold_args_info"
+
+description "The program partitions the secondary structure space into (basepair)distance classes according to\
+ two fixed reference structures. It expects a sequence and two secondary structures in dot-bracket notation as\
+ its inputs. For each distance class, the MFE representative, Boltzmann probabilities and Gibbs free energy is\
+ computed. Additionally, a stochastic backtracking routine allows to produce samples of representative suboptimal\
+ secondary structures from each partition\n\n"
+
+
+# Options
+section "General Options"
+sectiondesc="Below are command line options which alter the general behavior of this program\n\n"
+
+option "noconv" -
+"Do not automatically substitude nucleotide \"T\" with \"U\"\n\n"
+flag
+off
+
+option "numThreads" j
+"Set the number of threads used for calculations (only available when compiled with OpenMP support)\n\n"
+int
+optional
+
+section "Algorithms"
+
+option "partfunc" p
+"calculate partition function and thus, Boltzmann probabilities and Gibbs free energy\n\n"
+flag
+off
+
+
+option "stochBT" -
+"backtrack a certain number of Boltzmann samples from the appropriate k,l neighborhood(s)\n\n"
+int
+optional
+
+option "neighborhood" -
+"backtrack structures from certain k,l-neighborhood only, can be specified multiple times (<k>:<l>,<m>:<n>,...)\n\n"
+string
+typestr="<k>:<l>"
+multiple
+dependon="stochBT"
+
+option "pfScale" S
+"scaling factor for pf to avoid overflows\n\n"
+double
+optional
+
+option "noBT" -
+"do not backtrack structures, calculate energy contributions only\n\n"
+flag
+off
+
+option "circ" c
+"Assume a circular (instead of linear) RNA molecule.\n\n"
+flag
+off
+
+section "Model Details"
+
+option "temp" T
+"Rescale energy parameters to a temperature of temp C. Default is 37C.\n\n"
+double
+optional
+
+option "maxDist1" K
+"maximum distance to first reference structure"
+details="If this value is set all structures that exhibit a basepair distance greater than maxDist1 will\
+ be thrown into a distance class denoted by K=L=-1\n\n"
+int
+optional
+
+option "maxDist2" L
+"maximum distance to second reference structure"
+details="If this value is set all structures that exhibit a basepair distance greater than maxDist1 will\
+ be thrown into a distance class denoted by K=L=-1\n\n"
+int
+
+option "noTetra" 4
+"Do not include special tabulated stabilizing energies for tri-, tetra- and hexaloop hairpins. Mostly for testing.\n\n"
+flag
+off
+
+option "parameterFile" P
+"Read energy parameters from paramfile, instead of using the default parameter set.\n"
+details="A sample parameter file should accompany your distribution.\nSee the RNAlib\
+ documentation for details on the file format.\n\n"
+string
+typestr="paramfile"
+
+option "dangles" d
+"How to treat \"dangling end\" energies for bases adjacent to helices in free ends and multi-loops\n"
+details="\nWith -d2 dangling energies will be added for the bases adjacent to a helix on both sides
+ in any case.\nThe option -d0 ignores dangling ends altogether (mostly for debugging).\n\n"
+int
+default="2"
+values="0","2"
+
+option "noGU" -
+"Do not allow GU pairs\n\n"
+flag
+off
+
+option "noClosingGU" -
+"Do not allow GU pairs at the end of helices\n\n"
+flag
+off
+
+text "\nIf in doubt our program is right, nature is at fault.\nComments should be sent to\
+ rna@tbi.univie.ac.at.\n\n"
git://source.jalview.org / jabaws.git / blobdiff